Release notes - March 11, 2024

Recently published apps 

We’ve published the following new apps on BioData Catalyst powered by Seven Bridges:

• FusionInspector (v2.8.0), a tool that performs validation of fusion transcript predictions. FusionInspector is a part of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It takes a list of potential fusion genes (obtained by executing any fusion transcript prediction tool), extracts the genomic regions corresponding to the fusion partners, and creates mini-fusion-contigs that hold the gene pairs in the suggested fused orientation. The original reads align to these putative fusion contigs. In the fusion-gene context, fusion-supporting reads that would typically align as split reads or discordant pairs should align as concordant ‘normal’ reads. Reads that span fragments and reads containing fusion breakpoints that support each fusion, are recognized, reported, and scored accordingly. 
• Arriba (v2.4.0), a tool for the detection of gene fusions from RNA-Seq data. Arriba is designed to work with STAR aligner-processed data, and the post-alignment runtime is typically a few minutes long. Arriba does not require reducing the --alignIntronMax parameter of STAR to identify fusions resulting from focal deletions, in contrast to many other fusion detection methods that are based on STAR. Its intended application was in the context of clinical research. As such, high sensitivity and fast runtimes were crucial design requirements. Arriba can identify structural rearrangements other than gene fusions that may have clinical significance. These include viral integration sites, internal tandem duplications, whole exon duplications, and truncations of genes (i.e., breakpoints in introns and intergenic regions). 
• Arriba draw_fusions.R is an R script that comes with the Arriba gene fusions detection tool. This script produces visualizations of the transcripts involved in predicted fusions that are suitable for publication in terms of quality. For every predicted fusion, it creates a single page in the output PDF file. Each page contains information about the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and, if the fusion_transcript column has a value, an excerpt of the sequence around the breakpoint. 
• Parabricks RNA Pipeline, utilizing Parabricks toolkit v4.2.0. It is used for SNP and Indel discovery from RNAseq input data. 
• STAARpipeline PheWAS v0.9.6 which is used for analyzing WGS/WES sequencing data in PheWAS. 
• SRA to DRS converter workflow that converts SRA metadata to the DRS format for streamlined genomic data handling. This app is developed to streamline the conversion of Sequence Read Archive (SRA) metadata into Data Repository Service (DRS) URIs. It addresses the challenge faced by researchers in efficiently accessing and utilizing large genomic datasets stored in SRA format. By simplifying and automating this conversion, the app facilitates quicker and more effective genomic data analysis, thus accelerating research in the fields such as disease study and genetic discovery.

Recently updated apps 

We also updated the following apps: 

• DESeq2 tool (v1.40.1) that performs differential gene expression analysis across two or more study conditions. DESeq2 performs differential gene expression analysis using negative binomial generalized linear models. It analyzes estimated read counts from several samples, each belonging to one of two or more conditions under study, searching for systematic changes between conditions, as compared to within-condition variability.